Setup and Run Binary Mixtures with Martini
You need the following (1 script and 1 folder):
run_misctab_GMX16_cartes.sh
template-miscibility/
Submit a new mixture with:
./run_misctab_GMX16_cartes.sh BENZ 3 CHEX 2 293.15
where the arguments correspond to: 1) "BENZ" -> label of molecule_A; 2) "3" -> no. of beads of molecule_A; 3) "CHEX" -> label of molecule_B; 4) "2" -> no. of beads of molecule_B; 5) 293.15 -> temperature.
Note that the script uses a existing starting box named as:
3bead2bead-80008000.gro
if available or creates one from scratch; the name contains the no. of beads per molecule (3 beads for molecule_A, 2 beads for molecule_B) and the no. of molecules per molecules (8000 for molecule_A, 8000 for molecule_B). You can add yourself new pre-equilibrated starting boxes following the syntax above to the folder "template-miscibility/".
To adapt the script to run somewhere else than Cartesius:
- Potentially need to modify the "sbatch" line in
./run_misctab_GMX16_cartes.sh
- Check the header of
template-miscibility/setup_and_run_mixture.sh
which contains SBATCH commands such as:#SBATCH --partition=short
and command aliases such as:MDRUN="srun gmx_mpi mdrun"
.